sffinfocommand.cpp

   1 /*\r
   2  *  sffinfocommand.cpp\r
   3  *  Mothur\r
   4  *\r
   5  *  Created by westcott on 7/7/10.\r
   6  *  Copyright 2010 Schloss Lab. All rights reserved.\r
   7  *\r
   8  */\r
   9 \r
  10 #include "sffinfocommand.h"\r
  11 #include "endiannessmacros.h"\r
  12 \r
  13 //**********************************************************************************************************************\r
  14 \r
  15 SffInfoCommand::SffInfoCommand(string option)  {\r
  16         try {\r
  17                 abort = false;\r
  18                 hasAccnos = false;\r
  19                 \r
  20                 //allow user to run help\r
  21                 if(option == "help") { help(); abort = true; }\r
  22                 \r
  23                 else {\r
  24                         //valid paramters for this command\r
  25                         string Array[] =  {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};\r
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));\r
  27                         \r
  28                         OptionParser parser(option);\r
  29                         map<string, string> parameters = parser.getParameters();\r
  30                         \r
  31                         ValidParameters validParameter;\r
  32                         //check to make sure all parameters are valid for command\r
  33                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { \r
  34                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }\r
  35                         }\r
  36                         \r
  37                         //if the user changes the output directory command factory will send this info to us in the output parameter \r
  38                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }\r
  39                         \r
  40                         //if the user changes the input directory command factory will send this info to us in the output parameter \r
  41                         string inputDir = validParameter.validFile(parameters, "inputdir", false);        if (inputDir == "not found"){ inputDir = "";          }\r
  42 \r
  43                         sffFilename = validParameter.validFile(parameters, "sff", false);\r
  44                         if (sffFilename == "not found") { m->mothurOut("sff is a required parameter for the sffinfo command."); m->mothurOutEndLine(); abort = true;  }\r
  45                         else { \r
  46                                 splitAtDash(sffFilename, filenames);\r
  47                                 \r
  48                                 //go through files and make sure they are good, if not, then disregard them\r
  49                                 for (int i = 0; i < filenames.size(); i++) {\r
  50                                         if (inputDir != "") {\r
  51                                                 string path = hasPath(filenames[i]);\r
  52                                                 //if the user has not given a path then, add inputdir. else leave path alone.\r
  53                                                 if (path == "") {       filenames[i] = inputDir + filenames[i];         }\r
  54                                         }\r
  55         \r
  56                                         ifstream in;\r
  57                                         int ableToOpen = openInputFile(filenames[i], in, "noerror");\r
  58                                 \r
  59                                         //if you can't open it, try default location\r
  60                                         if (ableToOpen == 1) {\r
  61                                                 if (m->getDefaultPath() != "") { //default path is set\r
  62                                                         string tryPath = m->getDefaultPath() + getSimpleName(filenames[i]);\r
  63                                                         m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();\r
  64                                                         ableToOpen = openInputFile(tryPath, in, "noerror");\r
  65                                                         filenames[i] = tryPath;\r
  66                                                 }\r
  67                                         }\r
  68                                         in.close();\r
  69                                         \r
  70                                         if (ableToOpen == 1) { \r
  71                                                 m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();\r
  72                                                 //erase from file list\r
  73                                                 filenames.erase(filenames.begin()+i);\r
  74                                                 i--;\r
  75                                         }\r
  76                                 }\r
  77                                 \r
  78                                 //make sure there is at least one valid file left\r
  79                                 if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }\r
  80                         }\r
  81                         \r
  82                         accnosName = validParameter.validFile(parameters, "accnos", false);\r
  83                         if (accnosName == "not found") { accnosName = "";  }\r
  84                         else { \r
  85                                 hasAccnos = true;\r
  86                                 splitAtDash(accnosName, accnosFileNames);\r
  87                                 \r
  88                                 //go through files and make sure they are good, if not, then disregard them\r
  89                                 for (int i = 0; i < accnosFileNames.size(); i++) {\r
  90                                         if (inputDir != "") {\r
  91                                                 string path = hasPath(accnosFileNames[i]);\r
  92                                                 //if the user has not given a path then, add inputdir. else leave path alone.\r
  93                                                 if (path == "") {       accnosFileNames[i] = inputDir + accnosFileNames[i];             }\r
  94                                         }\r
  95         \r
  96                                         ifstream in;\r
  97                                         int ableToOpen = openInputFile(accnosFileNames[i], in, "noerror");\r
  98                                 \r
  99                                         //if you can't open it, try default location\r
 100                                         if (ableToOpen == 1) {\r
 101                                                 if (m->getDefaultPath() != "") { //default path is set\r
 102                                                         string tryPath = m->getDefaultPath() + getSimpleName(accnosFileNames[i]);\r
 103                                                         m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();\r
 104                                                         ableToOpen = openInputFile(tryPath, in, "noerror");\r
 105                                                         accnosFileNames[i] = tryPath;\r
 106                                                 }\r
 107                                         }\r
 108                                         in.close();\r
 109                                         \r
 110                                         if (ableToOpen == 1) { \r
 111                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();\r
 112                                                 //erase from file list\r
 113                                                 accnosFileNames.erase(accnosFileNames.begin()+i);\r
 114                                                 i--;\r
 115                                         }\r
 116                                 }\r
 117                                 \r
 118                                 //make sure there is at least one valid file left\r
 119                                 if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }\r
 120                         }\r
 121                         \r
 122                         if (hasAccnos) {\r
 123                                 if (accnosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a accnos file, you must have one for each sff file."); m->mothurOutEndLine(); }\r
 124                         }\r
 125                         \r
 126                         string temp = validParameter.validFile(parameters, "qfile", false);                     if (temp == "not found"){       temp = "T";                             }\r
 127                         qual = isTrue(temp); \r
 128                         \r
 129                         temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }\r
 130                         fasta = isTrue(temp); \r
 131                         \r
 132                         temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "F";                             }\r
 133                         flow = isTrue(temp); \r
 134                         \r
 135                         temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }\r
 136                         trim = isTrue(temp); \r
 137                         \r
 138                         temp = validParameter.validFile(parameters, "sfftxt", false);                           if (temp == "not found"){       temp = "F";                             }\r
 139                         sfftxt = isTrue(temp); \r
 140                 }\r
 141         }\r
 142         catch(exception& e) {\r
 143                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");\r
 144                 exit(1);\r
 145         }\r
 146 }\r
 147 //**********************************************************************************************************************\r
 148 \r
 149 void SffInfoCommand::help(){\r
 150         try {\r
 151                 m->mothurOut("The sffinfo command reads a sff file and extracts the sequence data.\n");\r
 152                 m->mothurOut("The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n");\r
 153                 m->mothurOut("The sff parameter allows you to enter the sff file you would like to extract data from.  You may enter multiple files by separating them by -'s.\n");\r
 154                 m->mothurOut("The fasta parameter allows you to indicate if you would like a fasta formatted file generated.  Default=True. \n");\r
 155                 m->mothurOut("The qfile parameter allows you to indicate if you would like a quality file generated.  Default=True. \n");\r
 156                 m->mothurOut("The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=False. \n");\r
 157                 m->mothurOut("The sfftxt parameter allows you to indicate if you would like a sff.txt file generated.  Default=False. \n");\r
 158                 m->mothurOut("The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values.  Default=True. \n");\r
 159                 m->mothurOut("The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s. \n");\r
 160                 m->mothurOut("Example sffinfo(sff=mySffFile.sff, trim=F).\n");\r
 161                 m->mothurOut("Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n");\r
 162         }\r
 163         catch(exception& e) {\r
 164                 m->errorOut(e, "SffInfoCommand", "help");\r
 165                 exit(1);\r
 166         }\r
 167 }\r
 168 //**********************************************************************************************************************\r
 169 \r
 170 SffInfoCommand::~SffInfoCommand(){}\r
 171 \r
 172 //**********************************************************************************************************************\r
 173 int SffInfoCommand::execute(){\r
 174         try {\r
 175                 \r
 176                 if (abort == true) { return 0; }\r
 177                 \r
 178                 for (int s = 0; s < filenames.size(); s++) {\r
 179                         \r
 180                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }\r
 181                         \r
 182                         int start = time(NULL);\r
 183                         \r
 184                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();\r
 185                         \r
 186                         string accnos = "";\r
 187                         if (hasAccnos) { accnos = accnosFileNames[s]; }\r
 188                         \r
 189                         int numReads = extractSffInfo(filenames[s], accnos);\r
 190 \r
 191                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");\r
 192                 }\r
 193                 \r
 194                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }\r
 195                 \r
 196                 //report output filenames\r
 197                 m->mothurOutEndLine();\r
 198                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();\r
 199                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }\r
 200                 m->mothurOutEndLine();\r
 201 \r
 202                 return 0;\r
 203         }\r
 204         catch(exception& e) {\r
 205                 m->errorOut(e, "SffInfoCommand", "execute");\r
 206                 exit(1);\r
 207         }\r
 208 }\r
 209 //**********************************************************************************************************************\r
 210 int SffInfoCommand::extractSffInfo(string input, string accnos){\r
 211         try {\r
 212                 \r
 213                 if (outputDir == "") {  outputDir += hasPath(input); }\r
 214                 \r
 215                 if (accnos != "")       {  readAccnosFile(accnos);  }\r
 216                 else                            {       seqNames.clear();               }\r
 217 \r
 218                 ofstream outSfftxt, outFasta, outQual, outFlow;\r
 219                 string outFastaFileName, outQualFileName;\r
 220                 string sfftxtFileName = outputDir + getRootName(getSimpleName(input)) + "sff.txt";\r
 221                 string outFlowFileName = outputDir + getRootName(getSimpleName(input)) + "flow";\r
 222                 if (trim) {\r
 223                         outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "fasta";\r
 224                         outQualFileName = outputDir + getRootName(getSimpleName(input)) + "qual";\r
 225                 }else{\r
 226                         outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "raw.fasta";\r
 227                         outQualFileName = outputDir + getRootName(getSimpleName(input)) + "raw.qual";\r
 228                 }\r
 229                 \r
 230                 if (sfftxt) { openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName); }\r
 231                 if (fasta)      { openOutputFile(outFastaFileName, outFasta);   outputNames.push_back(outFastaFileName); }\r
 232                 if (qual)       { openOutputFile(outQualFileName, outQual);             outputNames.push_back(outQualFileName);  }\r
 233                 if (flow)       { openOutputFile(outFlowFileName, outFlow);             outputNames.push_back(outFlowFileName);  }\r
 234                 \r
 235                 ifstream in;\r
 236                 in.open(input.c_str(), ios::binary);\r
 237                 \r
 238                 CommonHeader header; \r
 239                 readCommonHeader(in, header);\r
 240                 \r
 241                 int count = 0;\r
 242                 \r
 243                 //check magic number and version\r
 244                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }\r
 245                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }\r
 246         \r
 247                 //print common header\r
 248                 if (sfftxt) { printCommonHeader(outSfftxt, header); }\r
 249         \r
 250                 //read through the sff file\r
 251                 while (!in.eof()) {\r
 252                         \r
 253                         bool print = true;\r
 254                         \r
 255                         //read header\r
 256                         Header readheader;\r
 257                         readHeader(in, readheader);\r
 258                         \r
 259                         //read data\r
 260                         seqRead read; \r
 261                         readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);\r
 262                                 \r
 263                         //if you have provided an accosfile and this seq is not in it, then dont print\r
 264                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }\r
 265                         \r
 266                         //print \r
 267                         if (print) {\r
 268                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }\r
 269                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }\r
 270                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }\r
 271                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }\r
 272                         }\r
 273                         \r
 274                         count++;\r
 275                 \r
 276                         //report progress\r
 277                         if((count+1) % 10000 == 0){     m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }\r
 278                 \r
 279                         if (m->control_pressed) { count = 0; break;   }\r
 280                         \r
 281                         if (count >= header.numReads) { break; }\r
 282                 }\r
 283                 \r
 284                 //report progress\r
 285                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }\r
 286                 \r
 287                 in.close();\r
 288                 \r
 289                 if (sfftxt) {  outSfftxt.close();       }\r
 290                 if (fasta)      {  outFasta.close();    }\r
 291                 if (qual)       {  outQual.close();             }\r
 292                 if (flow)       {  outFlow.close();             }\r
 293                 \r
 294                 return count;\r
 295         }\r
 296         catch(exception& e) {\r
 297                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");\r
 298                 exit(1);\r
 299         }\r
 300 }\r
 301 //**********************************************************************************************************************\r
 302 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){\r
 303         try {\r
 304 \r
 305                 if (!in.eof()) {\r
 306 \r
 307                         //read magic number\r
 308                         char buffer[4];\r
 309                         in.read(buffer, 4);\r
 310                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));\r
 311                 \r
 312                         //read version\r
 313                         char buffer9[4];\r
 314                         in.read(buffer9, 4);\r
 315                         header.version = "";\r
 316                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i])); }\r
 317                                 \r
 318                         //read offset\r
 319                         char buffer2 [8];\r
 320                         in.read(buffer2, 8);\r
 321                         header.indexOffset =  be_int8(*(unsigned long int *)(&buffer2));\r
 322                         \r
 323                         //read index length\r
 324                         char buffer3 [4];\r
 325                         in.read(buffer3, 4);\r
 326                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));\r
 327                         \r
 328                         //read num reads\r
 329                         char buffer4 [4];\r
 330                         in.read(buffer4, 4);\r
 331                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));\r
 332                                 \r
 333                         //read header length\r
 334                         char buffer5 [2];\r
 335                         in.read(buffer5, 2);\r
 336                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));\r
 337                                         \r
 338                         //read key length\r
 339                         char buffer6 [2];\r
 340                         in.read(buffer6, 2);\r
 341                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));\r
 342                         \r
 343                         //read number of flow reads\r
 344                         char buffer7 [2];\r
 345                         in.read(buffer7, 2);\r
 346                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));\r
 347                                 \r
 348                         //read format code\r
 349                         char buffer8 [1];\r
 350                         in.read(buffer8, 1);\r
 351                         header.flogramFormatCode = (int)(buffer8[0]);\r
 352                         \r
 353                         //read flow chars\r
 354                         char* tempBuffer = new char[header.numFlowsPerRead];\r
 355                         in.read(&(*tempBuffer), header.numFlowsPerRead); \r
 356                         header.flowChars = tempBuffer;\r
 357                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }\r
 358                         delete[] tempBuffer;\r
 359                         \r
 360                         //read key\r
 361                         char* tempBuffer2 = new char[header.keyLength];\r
 362                         in.read(&(*tempBuffer2), header.keyLength);\r
 363                         header.keySequence = tempBuffer2;\r
 364                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }\r
 365                         delete[] tempBuffer2;\r
 366                                 \r
 367                         /* Pad to 8 chars */\r
 368                         unsigned long int spotInFile = in.tellg();\r
 369                         unsigned long int spot = (spotInFile + 7)& ~7;  // ~ inverts\r
 370                         in.seekg(spot);\r
 371                         \r
 372                 }else{\r
 373                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();\r
 374                 }\r
 375 \r
 376                 return 0;\r
 377         }\r
 378         catch(exception& e) {\r
 379                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");\r
 380                 exit(1);\r
 381         }\r
 382 }\r
 383 //**********************************************************************************************************************\r
 384 int SffInfoCommand::readHeader(ifstream& in, Header& header){\r
 385         try {\r
 386         \r
 387                 if (!in.eof()) {\r
 388                         \r
 389                         //read header length\r
 390                         char buffer [2];\r
 391                         in.read(buffer, 2);\r
 392                         header.headerLength = be_int2(*(unsigned short *)(&buffer));\r
 393                                                 \r
 394                         //read name length\r
 395                         char buffer2 [2];\r
 396                         in.read(buffer2, 2);\r
 397                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));\r
 398 \r
 399                         //read num bases\r
 400                         char buffer3 [4];\r
 401                         in.read(buffer3, 4);\r
 402                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));\r
 403                         \r
 404                         //read clip qual left\r
 405                         char buffer4 [2];\r
 406                         in.read(buffer4, 2);\r
 407                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));\r
 408                         \r
 409                         //read clip qual right\r
 410                         char buffer5 [2];\r
 411                         in.read(buffer5, 2);\r
 412                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));\r
 413                         \r
 414                         //read clipAdapterLeft\r
 415                         char buffer6 [2];\r
 416                         in.read(buffer6, 2);\r
 417                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));\r
 418 \r
 419                         //read clipAdapterRight\r
 420                         char buffer7 [2];\r
 421                         in.read(buffer7, 2);\r
 422                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));\r
 423                 \r
 424                         //read name\r
 425                         char* tempBuffer = new char[header.nameLength];\r
 426                         in.read(&(*tempBuffer), header.nameLength);\r
 427                         header.name = tempBuffer;\r
 428                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }\r
 429                         delete[] tempBuffer;\r
 430                         \r
 431                         /* Pad to 8 chars */\r
 432                         unsigned long int spotInFile = in.tellg();\r
 433                         unsigned long int spot = (spotInFile + 7)& ~7;\r
 434                         in.seekg(spot);\r
 435                         \r
 436                 }else{\r
 437                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();\r
 438                 }\r
 439 \r
 440                 return 0;\r
 441         }\r
 442         catch(exception& e) {\r
 443                 m->errorOut(e, "SffInfoCommand", "readHeader");\r
 444                 exit(1);\r
 445         }\r
 446 }\r
 447 //**********************************************************************************************************************\r
 448 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){\r
 449         try {\r
 450         \r
 451                 if (!in.eof()) {\r
 452         \r
 453                         //read flowgram\r
 454                         read.flowgram.resize(numFlowReads);\r
 455                         for (int i = 0; i < numFlowReads; i++) {  \r
 456                                 char buffer [2];\r
 457                                 in.read(buffer, 2);\r
 458                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));\r
 459                         }\r
 460         \r
 461                         //read flowIndex\r
 462                         read.flowIndex.resize(numBases);\r
 463                         for (int i = 0; i < numBases; i++) {  \r
 464                                 char temp[1];\r
 465                                 in.read(temp, 1);\r
 466                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));\r
 467                         }\r
 468         \r
 469                         //read bases\r
 470                         char* tempBuffer = new char[numBases];\r
 471                         in.read(&(*tempBuffer), numBases);\r
 472                         read.bases = tempBuffer;\r
 473                         if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases);  }\r
 474                         delete[] tempBuffer;\r
 475 \r
 476                         //read qual scores\r
 477                         read.qualScores.resize(numBases);\r
 478                         for (int i = 0; i < numBases; i++) {  \r
 479                                 char temp[1];\r
 480                                 in.read(temp, 1);\r
 481                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));\r
 482                         }\r
 483         \r
 484                         /* Pad to 8 chars */\r
 485                         unsigned long int spotInFile = in.tellg();\r
 486                         unsigned long int spot = (spotInFile + 7)& ~7;\r
 487                         in.seekg(spot);\r
 488                         \r
 489                 }else{\r
 490                         m->mothurOut("Error reading."); m->mothurOutEndLine();\r
 491                 }\r
 492 \r
 493                 return 0;\r
 494         }\r
 495         catch(exception& e) {\r
 496                 m->errorOut(e, "SffInfoCommand", "readSeqData");\r
 497                 exit(1);\r
 498         }\r
 499 }\r
 500 //**********************************************************************************************************************\r
 501 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {\r
 502         try {\r
 503         \r
 504                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;\r
 505                 out << "Version: " << header.version << endl;\r
 506                 out << "Index Offset: " << header.indexOffset << endl;\r
 507                 out << "Index Length: " << header.indexLength << endl;\r
 508                 out << "Number of Reads: " << header.numReads << endl;\r
 509                 out << "Header Length: " << header.headerLength << endl;\r
 510                 out << "Key Length: " << header.keyLength << endl;\r
 511                 out << "Number of Flows: " << header.numFlowsPerRead << endl;\r
 512                 out << "Format Code: " << header.flogramFormatCode << endl;\r
 513                 out << "Flow Chars: " << header.flowChars << endl;\r
 514                 out << "Key Sequence: " << header.keySequence << endl << endl;\r
 515                         \r
 516                 return 0;\r
 517         }\r
 518         catch(exception& e) {\r
 519                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");\r
 520                 exit(1);\r
 521         }\r
 522 }\r
 523 //**********************************************************************************************************************\r
 524 int SffInfoCommand::printHeader(ofstream& out, Header& header) {\r
 525         try {\r
 526                 \r
 527                 out << ">" << header.name << endl;\r
 528                 out << "Run Prefix: " << endl;\r
 529                 out << "Region #:  " << endl;\r
 530                 out << "XY Location: " << endl << endl;\r
 531                 \r
 532                 out << "Run Name:  " << endl;\r
 533                 out << "Analysis Name:  " << endl;\r
 534                 out << "Full Path: " << endl << endl;\r
 535                 \r
 536                 out << "Read Header Len: " << header.headerLength << endl;\r
 537                 out << "Name Length: " << header.nameLength << endl;\r
 538                 out << "# of Bases: " << header.numBases << endl;\r
 539                 out << "Clip Qual Left: " << header.clipQualLeft << endl;\r
 540                 out << "Clip Qual Right: " << header.clipQualRight << endl;\r
 541                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;\r
 542                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;\r
 543                 \r
 544                 return 0;\r
 545         }\r
 546         catch(exception& e) {\r
 547                 m->errorOut(e, "SffInfoCommand", "printHeader");\r
 548                 exit(1);\r
 549         }\r
 550 }\r
 551 \r
 552 //**********************************************************************************************************************\r
 553 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {\r
 554         try {\r
 555                 \r
 556                 out << "FlowGram: ";\r
 557                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }\r
 558                 \r
 559                 out << endl <<  "Flow Indexes: ";\r
 560                 int sum = 0;\r
 561                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }\r
 562                 \r
 563                 //make the bases you want to clip lowercase and the bases you want to keep upper case\r
 564                 for (int i = 0; i < header.clipQualLeft; i++) { read.bases[i] = tolower(read.bases[i]); }\r
 565                 for (int i = header.clipQualLeft; i < (header.clipQualRight-header.clipQualLeft); i++) {   read.bases[i] = toupper(read.bases[i]);  }\r
 566                 for (int i = (header.clipQualRight-header.clipQualLeft); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }\r
 567                 \r
 568                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";\r
 569                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }\r
 570         \r
 571                 \r
 572                 out << endl << endl;\r
 573                 \r
 574                 return 0;\r
 575         }\r
 576         catch(exception& e) {\r
 577                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");\r
 578                 exit(1);\r
 579         }\r
 580 }\r
 581 //**********************************************************************************************************************\r
 582 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {\r
 583         try {\r
 584                 \r
 585                 string seq = read.bases;\r
 586                 \r
 587                 \r
 588                 if (trim) {\r
 589                         seq = seq.substr(header.clipQualLeft, (header.clipQualRight-header.clipQualLeft));\r
 590                 }else{\r
 591                         //if you wanted the sfftxt then you already converted the bases to the right case\r
 592                         if (!sfftxt) {\r
 593                                 //make the bases you want to clip lowercase and the bases you want to keep upper case\r
 594                                 for (int i = 0; i < header.clipQualLeft; i++) { seq[i] = tolower(seq[i]);  }\r
 595                                 for (int i = header.clipQualLeft; i < (header.clipQualRight-header.clipQualLeft); i++) {   seq[i] = toupper(seq[i]);  }\r
 596                                 for (int i = (header.clipQualRight-header.clipQualLeft); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }\r
 597                         }\r
 598                 }\r
 599                 \r
 600                 out << ">" << header.name << endl;\r
 601                 out << seq << endl;\r
 602                 \r
 603                 return 0;\r
 604         }\r
 605         catch(exception& e) {\r
 606                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");\r
 607                 exit(1);\r
 608         }\r
 609 }\r
 610 \r
 611 //**********************************************************************************************************************\r
 612 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {\r
 613         try {\r
 614                 \r
 615                 if (trim) {\r
 616                         out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;\r
 617                         for (int i = header.clipQualLeft; i < (header.clipQualRight-header.clipQualLeft); i++) {   out << read.qualScores[i] << '\t';  }\r
 618                 }else{\r
 619                         out << ">" << header.name << " length=" << read.qualScores.size() << endl;\r
 620                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }\r
 621                 }\r
 622                 \r
 623                 out << endl;\r
 624                 \r
 625                 return 0;\r
 626         }\r
 627         catch(exception& e) {\r
 628                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");\r
 629                 exit(1);\r
 630         }\r
 631 }\r
 632 \r
 633 //**********************************************************************************************************************\r
 634 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {\r
 635         try {\r
 636                 \r
 637                 out << ">" << header.name << endl;\r
 638                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }\r
 639                 out << endl;\r
 640                 \r
 641                 return 0;\r
 642         }\r
 643         catch(exception& e) {\r
 644                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");\r
 645                 exit(1);\r
 646         }\r
 647 }\r
 648 //**********************************************************************************************************************\r
 649 int SffInfoCommand::readAccnosFile(string filename) {\r
 650         try {\r
 651                 //remove old names\r
 652                 seqNames.clear();\r
 653                 \r
 654                 ifstream in;\r
 655                 openInputFile(filename, in);\r
 656                 string name;\r
 657                 \r
 658                 while(!in.eof()){\r
 659                         in >> name; gobble(in);\r
 660                                                 \r
 661                         seqNames.insert(name);\r
 662                         \r
 663                         if (m->control_pressed) { seqNames.clear(); break; }\r
 664                 }\r
 665                 in.close();             \r
 666                 \r
 667                 return 0;\r
 668         }\r
 669         catch(exception& e) {\r
 670                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");\r
 671                 exit(1);\r
 672         }\r
 673 }\r
 674 //**********************************************************************************************************************/\r